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Author Topic:   An ID hypothesis: Front-loaded Evolution
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 112 of 216 (653730)
02-23-2012 11:29 PM
Reply to: Message 101 by Wounded King
02-23-2012 11:35 AM


Re: DNA / Protein disjunction
On another related point, if you take the mRNA coding for the sequence that Genomicus chose and blast that against the Prokaryota then you get no significant hits.
Protein sequence comparisons allow us to look back over longer periods of time than DNA/mRNA sequences. Since we're talking about deep time here, I don't think it's even appropriate to do a BLAST search with an mRNA query.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 113 of 216 (653731)
02-23-2012 11:34 PM
Reply to: Message 112 by Genomicus
02-23-2012 11:29 PM


General Response to Objections, above
For the record: I kinda buried my primary post with replies to individual comments, so my general response to objections to FLE can be found in my brief essay above.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 115 of 216 (653736)
02-24-2012 12:30 AM
Reply to: Message 114 by Dr Jack
02-23-2012 11:52 PM


Re: Catching up
You don't have good E-values. 1e-5 is not a good E-value, it's bordering on noise.
Well, consider that:
a. The E-values are not 1e-05. They are a bit less than that.
b. An E-value of 1e-05 is not "bordering on noise" IMHO. Various investigators have used the E-value of 1e-04 as the cutoff value, yet their findings have been accepted by the scientific community.
Of course, we have to look at the broader biological context here, too. In fact, I'm more than willing that the matches don't indicate front-loading. That's why I'm curious on this: do you think we'll ever find significant structural or sequence homologs of PAX6 in prokaryotes?
To illustrate my point about E-values, try blasting P11388 against the prokaryotes (P11388 being human DNA topoisomerase ii-alpha), here where there is genuine, deep-rooted, homology you get E-values in the sub 1e-35 range across a stack of different bacterial species from the various branches of bacterial life.
I'm perfectly aware about the statistics of database matches.
Edited by Genomicus, : No reason given.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 119 of 216 (653745)
02-24-2012 3:46 AM
Reply to: Message 116 by Dr Adequate
02-24-2012 12:58 AM


Re: General Response to Objections
No, no, you misunderstand me. Let's hypothesize that they're both front-loaded. Fine. But at some point branching has to take place. One lineage has to go one way and do photosynthesis, while the other goes the other way and does hemoglobin. Now this itself, on the face of it, cannot be preprogrammed. The reason why one lineage develops one way and another develops in another way cannot be the result of their common genetic heritage.
Yes, but front-loading isn't about pre-programming something. It's about "stacking the deck," and anticipating the rise of plants and animals, for example. Simply put, if we start with an origin population of cells, which contain genes necessary for the development/function of plants and animals; next, this initial population separates into two populations. Then, deletion events in one population removes the animal genes, say, so that we just end up with plants. Alternatively, the front-loading designers could have designed such a population from the start: where some cells have genes for plants, and others have genes for animals.

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Replies to this message:
 Message 124 by Dr Adequate, posted 02-24-2012 4:24 AM Genomicus has replied
 Message 128 by Trixie, posted 02-24-2012 4:44 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 120 of 216 (653747)
02-24-2012 3:56 AM
Reply to: Message 117 by Dr Adequate
02-24-2012 2:17 AM


Re: General Response to Objections
Actually, I think it is.
Well, not when seen in the context of other biological features. In my little essay, I showed how (a) it is feasible for specific proteins to be front-loaded; (b) it is feasible for specific molecular machines to be front-loaded; and (c) how specific biochemical pathways can plausibly front-loaded. Thus, demanding that I explain the origin of the eye through FLE seems to be pushing the goal-posts back. The FLE hypothesis is just in its infancy; demanding that we produce a teleological hypothesis for the origin of the eye, at this point, seems a little premature, to me at least.

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 Message 117 by Dr Adequate, posted 02-24-2012 2:17 AM Dr Adequate has replied

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 Message 127 by Dr Adequate, posted 02-24-2012 4:39 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 122 of 216 (653749)
02-24-2012 4:02 AM
Reply to: Message 121 by Trixie
02-24-2012 3:58 AM


Re: You need to deal with this
Are you now withdrawing your claim that the BLASTP results suggest that eyes were anticipated?
Yes.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 131 of 216 (653760)
02-24-2012 4:55 AM
Reply to: Message 118 by PaulK
02-24-2012 2:20 AM


Re: General Response to Objections
It was valid enough that Darwin thought it to be worth answering. The usual problem is that creationists quote the argument but ignore the response, giving a deeply misleading impression of what Darwin was saying.
See my response to Dr Adequate, above.
I think that recognising the problems with front-loading, even if they are expressed a little vaguely is an important part of this discussion.
True.
Now this is where we see problems with your arguments.
Does designing rhodopsin into the first life significantly increase the chance of eyes evolving ? Nothing you say really addresses this point. You say it does, but it really isn't clear why you think that.
Can we really say that rhodopsin specifically would be used ? It's available for co-option, sure, but is it the only possibility ? How likely is it to be the only possibility or even the most available option when eyes do evolve ? We do need to be careful to avoid thinking that the way things work now is the only possible way, especially in the context of this discussion since it would bias the argument in favour of front-loading.
Designing rhodopsin (or a homolog of rhodopsin) in the first genomes increases the likelihood that eyes will emerge precisely because the blind watchmaker doesn't have to tinker around with a totally unrelated protein, gradually transforming it into a protein that can be used for vision. If, however, rhodopsin (and other vision-related proteins) is designed into the first genomes, the fundamental ingredients for eye evolution are already in place, biasing evolution in favor of eye evolution. Few novel genes would have to evolve, and this significantly increases the chances of eye evolution.
Rhodopsin would be available for co-option, but would it be the only possibility? Possibly the blind watchmaker would "generate" a protein that would then be co-opted into a vision-related function. But this would be an extra step: the blind watchmaker would have to duplicate an existing gene, modify it such that its function is compatible with a vision system, and then it'd be co-opted. These extra steps make it less likely for the eye to evolve in the absence of front-loading.
According to Wikipedia (not the best source, I know but usually OK on science and more accessible to the lay public) bacterial rhodopsins may have an evolutionary relationship with visual rhodopsins, but they may not. Doesn't this make it a rather poor example of possible "front-loading" ?
From Wikipedia:
"Bacteriorhodopsin belongs to a family of bacterial proteins related to vertebrate rhodopsins, the pigments that sense light in the retina." (Emphasis added)
Anyways, it was meant as an analogy - just to get the idea across.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 132 of 216 (653762)
02-24-2012 5:02 AM
Reply to: Message 124 by Dr Adequate
02-24-2012 4:24 AM


Re: General Response to Objections
Well, this would be a bit of a climb-down. Are you going to give up on common ancestry?
How on earth would this be incompatible in any way with common ancestry? You'd simply design cell population A with genes that would be later used by plants, and cell population B with genes that would be later used by animals. These two populations, on the whole, would be genetically related, with the exception of the different plant/animal genes.
This "deletion event" happens to plants, but not animals. When they start off with the same genome. What causes this to happen?
Not meaning to dodge this question, but I think Mr Jack has answered this question succinctly.
If you do wish to abandon common ancestry then we have a whole 'nother discussion on our hands.
I really don't see how I seem to be abandoning common ancestry.

This message is a reply to:
 Message 124 by Dr Adequate, posted 02-24-2012 4:24 AM Dr Adequate has replied

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 Message 139 by Dr Adequate, posted 02-24-2012 5:17 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 133 of 216 (653764)
02-24-2012 5:05 AM
Reply to: Message 128 by Trixie
02-24-2012 4:44 AM


Re: General Response to Objections
Obviously your argument in favour of front-loading requires an entity or entities to "anticipate", to be the "front-loading designers". It now seems that it may require constant intervention in the form of "tinkering".
Not at all. Perhaps I'm not being clear here. I'm simply saying that the first life forms that were seeded on earth could contain different sets of genes, one for plants, and one for animals. Evolution would follow from there, shaped around the initial constraints. There is no constant intervention/tinkering from any intelligence.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 134 of 216 (653765)
02-24-2012 5:09 AM
Reply to: Message 127 by Dr Adequate
02-24-2012 4:39 AM


Re: General Response to Objections
Well, you know, if you want to develop the hypothesis, and you find you need another few years to get it right, then you go for it. As I said, I do admire your ambition. You're almost certainly wrong, but science would not progress unless people pursued seemingly crazy ideas. I've pursued a few of those myself.
But, you can't expect anyone to accept your ideas when they're in their present half-formed condition. All I can do is wish you the very best of luck. But if you can't explain the evolution of the eye, then presently we have to say that your hypothesis has failed to do what it is meant to do, namely explain evolution.
Remember, the purpose of this discussion - at least my purpose of this discussion - and that is for the FLE hypothesis to be refined. Before submitting any FLE hypothesis to the scientific community, it's not a bad idea to see what the bio guys and gals over here at EvC think about the FLE hypothesis, dontcha think? This helps in pointing out the weak spots and strong spots in the hypothesis, and indicates which parts need to be developed more rigorously.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 140 of 216 (653771)
02-24-2012 5:21 AM
Reply to: Message 136 by Dr Jack
02-24-2012 5:14 AM


Re: The tree of life vs. separate pools
I'm sure you're familiar with this image or others very like it. It's the biological tree of life showing the relationship between the major domains and kingdoms. You'll note that plants and animals are actually quite close together, and far removed from the two groups of prokaryotes. Were there separate seed populations of prokaryotes, one for plants, and another for animals shouldn't we expect to see these pools group with their descendent multi-cellular forms?
Yes, and based on phylogenetic considerations, I don't think my idea of two different initial populations is tenable.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 142 of 216 (653773)
02-24-2012 5:24 AM
Reply to: Message 139 by Dr Adequate
02-24-2012 5:17 AM


Re: General Response to Objections
Something has to make the difference. This something, by your hypothesis, cannot lie in the genome. Where, then, does it lie?
Chance. What's stopping animal genes in one lineage from being deleted? What's stopping a plant lineage to start developing, built around plant genes, and thus animal genes would be eliminated in this lineage (or become pseudogenes)?

This message is a reply to:
 Message 139 by Dr Adequate, posted 02-24-2012 5:17 AM Dr Adequate has replied

Replies to this message:
 Message 143 by Dr Adequate, posted 02-24-2012 5:30 AM Genomicus has replied
 Message 144 by Tangle, posted 02-24-2012 5:33 AM Genomicus has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 145 of 216 (653777)
02-24-2012 5:40 AM
Reply to: Message 143 by Dr Adequate
02-24-2012 5:30 AM


Re: General Response to Objections
OK, that's a new factor in your hypothesis. Chance decides it.
But in that case, shouldn't we stop calling your hypothesis front-loaded evolution, when it is, according to you, just how the dice happened to fall? What I understood by "front-loaded evolution" is that the outcome was inevitable. If, instead, it is random, then perhaps you should think of another name for it.
Chance has always been a factor in the FLE hypothesis. Biology is a probabilistic science - the outcome was not inevitable, but certainly the odds were considerably in its favor.
Consider the following example: the last common ancestor of plants and animals have genes x (an animal gene) and y (a plant gene). In one of these lineages, a series of mutations occur, generating a new morphological structure such that gene x is necessary for the existence of the new lineage. Gene y is dispensable, and so it is lost in this lineage. An analogous process occurs in a second lineage, albeit in reverse: instead of gene y being lost, gene x is lost.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 146 of 216 (653778)
02-24-2012 5:42 AM
Reply to: Message 144 by Tangle
02-24-2012 5:33 AM


Re: General Response to Objections
Now I'm properly confused; I thought the point was that the dice are loaded?
If by "the dice were loaded" you mean the outcome was inevitable, then no. But under the FLE hypothesis, the outcome that resulted was far more probable than in the absence of front-loading. The first genomes anticipated the origin of plants and animals, for example.

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Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 150 of 216 (653783)
02-24-2012 6:05 AM
Reply to: Message 148 by Dr Adequate
02-24-2012 5:58 AM


Re: The Role Of Chance
Then you would have done well to mention this in your OP instead of waiting 'til now.
Actually, I thought that was sufficiently clear: that the blind watchmaker tinkers with the initial constraints, and it shapes its designs around those initial constraints.
But if chance is a factor, then in what sense is evolution front-loaded? If it is purely a matter of chance that evolution produced humans and tigers rather than bumblegriffs and hippodores, then where is the front-loading?
Multi-cellular life forms, plants and animals, possibly invertebrates and vertebrates; specific taxonomic classes could be anticipated by the first genomes, but they weren't necessarily front-loaded. Still, any "anticipation" would make the appearance of a specific biological feature much more probable. One reason chance is a factor is because you can't stop the blind watchmaker - but you can put it to work for you if you start with right initial constraints.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 148 by Dr Adequate, posted 02-24-2012 5:58 AM Dr Adequate has replied

Replies to this message:
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